Master Thesis Hydronumerical Modelling of Nutrients and Oxygen in Ciénaga Grande de Santa Marta, Colombia In fulfillment of the requirements for the degree of Master of Science (M.Sc.) in Water Resources and Environmental Management At the faculty of Civil Engineering and Geodetic Sciences of Leibniz Universität Hannover Marcos Carvajalino Fernández Mat. Nr: 3040980 Date of presentation: 30. September 2015 Supervisor: M.Sc. Oliver Lojek Examiners: Prof. Dr.-Ing T. Schlurmann Prof. Dr.-Ing A. Hildebrandt This page intentionally left blank. II Dedicated to my grandmother, Amalia Isabel Sánchez Santiago. Who was always there for me and taught me that true happiness comes from loving and caring for someone else. You will always be by my side. This page intentionally left blank. IV DECLARATION I hereby declare that the topic handed out on September 30th of 2015 as Master Thesis, entitled "Hydronumerical modelling of nutrients and oxygen in Ciénaga Grande de Santa Marta, Colombia", was authored entirely and independently by me, Marcos Antonio Carvajalino Fernández (Mat. Nr: 3040980). This academic work is the outcome of a joint effort between Instituto de Investigaciones Marinas y Costeras "José Benito Vives de Andreis" (INVEMAR), Franzius-Institute for Hydraulic, Estuarine and Coastal Engineering and the author. It was developed under the supervision of professionals from Franzius-Institute and INVEMAR. However, the conclusions presented in this document correspond to my assessment of the facts and do not necessarily reflect the opinion of any of the involved institutions. I also declare that I have written this document without extracting sections from other sources (including electronic media and online sources). All the documents used as references for the present report have been thoroughly cited and identified. This work has not been submitted to any other examination board in this or any other university in order to obtain an academic degree. I am aware that a false declaration could have legal implications. Therefore, I agree to the submission of this document to external services for plagiarism check. MARCOS CARVAJALINO FERNÁNDEZ Hannover, Germany. 30. Sept. 2015 V This page intentionally left blank. VI ACKNOWLEDGEMENTS First and foremost, I would like to thank INVEMAR and Franzius-Institute for placing their trust in me and accepting my research proposal. Betting on this project was a leap of faith since we all knew from start that information was scarce and scattered along many institutions and a considerable effort had to be made in order to develop an integrated tool like the one proposed. Thanks for encouraging young professionals into pursuing their own ideas. I would like to thank Deutscher Akademischer Austausch Dienst (DAAD) for financing my studies in Germany during the past two years. This has been the most nourishing experience of my life both academically and culturally. I am specially indebted to M.Sc. Luis Fernandes (Actionmodulers Inc.) for his constant technical support regarding MOHID modelling system and Eduardo Jauch (Technical University of Lisbon) for his help in compiling MOHID Water in Linux Operating Systems. My academic supervisor M.Sc. Oliver Lojek was always eager to help me with administrative pro- cedures and coping with my ever increasing computational needs, even when it meant lending me his personal desktop PC. Thanks for easing all the thesis process so I could focus on the important aspects of the project. I would also like to express my gratitude to the staff from CAM and GEO programs at INVEMAR, specially Ostin Garcés and Carlos Carbonó for their help during the field campaigns. Thanks to Janet Vivas and Martha Bastidas as the direct contacts from both programs for facilitating the access to INVEMAR datasets. M.Sc. Jorge Corrales was so kind as to lend us his company’s flowmeter when we had problems with ours, without it we could have not finished the data gathering on time. Many people offered me their professional advice during the project, thanks to M.Sc. Jorge Mazenett, Luís Vanegas and Dr. Andrés Osorio Arias (Universidad Nacional de Colombia) for giving me some hints and sharing some of their experience with me. Special thanks to my colleagues Jesús Casado, Raúl Villanueva, Erika Álvarez, Fernanda Scholz and Larisa Tarasova for the company during all this experience and the countless coffee/döner breaks discussing our projects’ issues. Last but not least, I would like to thank my family for their constant support and advice throughout the unique (and sometimes scary) experience of living and studying in a foreign country. You were the true pillar of this achievement and I could have never done it without you. VII This page intentionally left blank. VIII ABSTRACT A numerical model for the simulation of hydrodynamic, conservative substances and nutrient/oxygen transport inside a selected domain of Ciénaga Grande de Santa Marta lagoon complex (CGSM-LC) and its adjacent continental margin was developed in MOHID Water Modelling System as the first large scale water quality modelling initiative from INVEMAR in the Colombian Caribbean. The model performed satisfactorily well in long-term (yearly) simulations of water level fluctuations and salinity patterns inside the estuary area, reporting daily level changes of around 3 cm to 4 cm and velocities of around 1 m s−1 in the seawater inlet of the system and less than 5 cm s−1 in most of the lagoons. Good representation of monthly patterns reported for the system was achieved for wet and transition climatic periods, however the model still needs to be adjusted to adequately simulate the dry weather conditions. Flow patterns in the system shown a marginal tidal influence in the Northeastern part of the system with a tidal excursion of approximately 4 km during flood tides, with the salt wedge reaching the zone of El Boquerón island before the slack tide and water retreat. In the rest of the system, flow patterns are dominated by the freshwater inflows and wind shear stresses, showing microscale phenomena like water reversals and short-life eddies in the North and Southwest areas of the main lagoon. Flow in CGSM main lagoon is very slow, with residence times of more than 7 months and probably even reaching a year, this situation is even worse in Pajarales lagoon where almost no net water flushing can be observed, operating mostly as an evaporative system. These long residence times make both systems specially sensitive to the accumulation of recalcitrant pollutants. Nutrient and Oxygen simulations for 5 d periods in both dry and wet weather conditions were performed, representing daily biochemical cycles in concordance with previous descriptive works in the area, with a cyclic daily pattern of nutrient consumption by phytoplankton during the day and oxygen depletion during the night. One major drawback in the current state of the model is that it is not including the bacterial biomass that is intervening in the nutrient cycles due to lack of field information on this parameter. Without this element, the nitrification schemes are not complete and an Ammonia accumulation trend can be observed in the results. Further calibration and validation procedures, inclusion of the bacteria component, as well as long term simulations to verify that the model is able to replicate seasonal patterns for these non-conservative variables are planned extensions for the near future. IX This page intentionally left blank. X CONTENTS 1 Introduction1 1.1 Ciénaga Grande de Santa Marta Lagoon Complex..................1 1.2 Motivation.......................................5 1.3 Objectives.......................................7 2 Domain description9 2.1 Institutional framework and previous studies.....................9 2.2 Physical description.................................. 10 2.2.1 Bathymetry.................................. 12 2.2.2 Bottom material................................ 14 2.3 Environmental conditions............................... 15 2.3.1 Atmospheric dynamics............................. 15 2.3.2 Hydrology................................... 17 2.3.3 Pollution sources................................ 18 2.4 Ocean conditions.................................... 19 2.4.1 Internal waves................................. 22 3 Materials and methods 23 3.1 Model domain and software selection......................... 23 3.2 MOHID model description............................... 25 3.3 Hydrodynamic model................................. 27 3.3.1 Grid selection................................. 27 3.3.2 Boundary conditions and input data...................... 28 3.3.3 Residence time calculation........................... 34 3.4 Nutrients and oxygen model.............................. 34 3.5 Simulations....................................... 35 3.6 Calibration....................................... 36 4 Results and discussion 37 4.1 Input data preprocessing................................ 37 4.1.1 Bathymetry.................................. 37 XI 4.1.2 Atmospheric variables............................. 39 4.1.3 Hydrological variables............................. 41 4.1.4 Tide verification................................ 43 4.2 Stability and convergence............................... 44 4.3 Temporal patterns of hydrodynamic variables..................... 46 4.3.1 Water level................................... 46 4.3.2 Water velocity................................. 47 4.4 Flow patterns in the system.............................. 48 4.5 Residence times...................................