Background Water systems in Cyprus are under increasing pressure from human activity, and changing weather patterns and hydrological conditions. The availability of water has been in recent years the most pressing issue because of the ongoing drought, while urban non-point pollution has been one of the main sources of pressure. The project area, Kalo Horio catchment, drains into the two Larnaca salt lakes, which form Natura 2000 site. The lakes are the second largest in size and importance in Cyprus after the Akrotiri salt lake in Limassol. Despite its ecological importance, the site is under severe pressure from human activities, such as industrial pollution from the Aradipou industrial zone, non-point pollution from agricultural and farming activities, the Larnaca airport and the Larnaca Sewage Treatment Plant. Objectives The overall goal of the WATER project was to strengthen the scientific foundation of water management programmes. To achieve this goal, the project planned to establish and demonstrate an innovative set of methods and tools for the design and implementation of programmes for the preservation of the high environmental quality and good ecological status of water bodies. The major technical objective of the project was to establish and implement detailed, distributed dynamic simulation models in terms of a dynamic water budget (based on the natural climate-driven hydrological cycle, anthropogenic demand and allocations), resulting in water availability and quality criteria. It introduced the concept of the Total Maximum Daily Loads (TMDLs) as a means of enhancing the procedures for water quality management. Equally important was the aim of the project to inform and involve stakeholders and key players that influence or are affected by water management decisions. Therefore great emphasis was given to dissemination of the project tools and methods through a pilot implementation action, which promoted the proposed tools to a big audience of stakeholders. Results The WATER project developed and demonstrated a quantitative methodology for the integrated management of water quality at the river basin of Kalo Horio, Larnaca. Specifically, the project team purchased and installed the BASINS4 System which has been developed by US-EPA and which integrates hydrological, GIS, TMDLs formulation and ecological quality models. The system was used to prepare and implement the foreseen modeling activities, scenario analysis and TMDL development. The modeling activity was supported by a detailed monitoring and assessment program which involved ecological, water quality and hydrological monitoring, functions analysis and the establishment of ecological and water quality criteria. The initial implementation of the software generated five geospatial data input files: a Digital Elevation Model of the area, a stream flow network, a catchment and sub catchment hydrological map, a land-use map and weather data. A key initial deliverable was the establishment of a 5-year water flow and water balance time series supplemented by water quality calculations at a daily temporal resolution. During the initial implementation of the model, available data regarding the Kalo Horio river basin was shown to be incomplete (especially GIS data and metadata, water flow rates and characterisation of pollutant sources) which were completed through extensive field work. The sub-catchment boundaries and the stream network were redesigned, water flow rates were determined, point sources and their pollutant release rates were identified (with the use of a questionnaire and interviews with industry and farmers), non-point sources of pollution were determined and water quality was monitored. Around 400 water samples were collected and analysed, which were used to assess the status of the site and to calibrate the model. Furthermore, the project determined water quality parameters that are key to maintaining good ecological status in the area's water bodies (i.e. average extent of the flooding zone, nutrient levels, Dissolved Oxygen levels, TSS (total suspended solids), salinity range, annual flooding duration, TOC (total organic carbon), E.Coli, BOD) with an emphasis on the Larnaca Salt Lake complex. The most important physicochemical parameters for the preservation of key functions of the Salt Lake's water bodies were identified. Limiting factors (most importantly water quality indicators), with their upper and lower limits for each quality indicator, were also identified. These were then used to set the target conditions. Lastly the pollutant sources that fall under the IPPC directive and other pollution sources in the area were registered and emission rates were calculated. Total Maximum Daily Loads (TMDLs) were assessed at four key locations: the main salt lake of Larnaca, north and south sides; Phaneromeni's canal; Vergina canal; and the Western Lake, where Bryophyta was identified for the first time in Cyprus through the project’s monitoring actions). Assessments were made for five key parameters: BOD, F. Coli, nitrates-nitrites, ammonia and phosphorus. In addition to the scenario based on the current land uses, two other scenarios were developed with the use of the BASINS4 system to study the influence of climatic changes and foreseen land-use changes on the salt lake's hydrology and water quality conditions. In order to facilitate the preparation of water management measures, a new optimisation model was developed for the purposes of the project, using the What's Best! software. A back and forth process between the optimisation model and BASINS4, produced a preferred management scenario for the Kalo Horio catchment and prioritised management measures. Trade-off curves were used for this purpose which were based on considerations of acceptance of countermeasure technologies, specific budget restrictions, and environmental improvement targets such as a 15 % removal efficiency in all key pollutants, 30% removal efficiency in NO3 contaminant, and a 30% removal efficiency in BOD contaminant were produced by BASINS4 using the TMDL formulations. Ten possible countermeasure technologies or best management practices were evaluated: CSO (Combined Sewer Overflow) Retention Basins, constructed wetlands, water quality inlet, infiltration drain fields, street cleaning, field strips, porous pavement, grassed swale, removal of farming zones, and abandonment of cultivation. Stakeholder consultations, with the use of a questionnaire, were organised. On the basis of these inputs, the management scenario that was suggested for the Kalo Horio area was the ‘15% removal rate in all key pollutants’, which includes the following five management practices: street cleaning, oil traps and filters in the area of Vergina, livestock management practices to achieve a 70% reduction of nutrient pollutant load from livestock, creation of a buffer zone of up to 300m between agricultural land use and the salt lakes, and enforcement of good management practices at construction sites to prevent erosion and the runoff of particulates and pollutants. Potential users of the software from the Department of Environment, Water Development Department, Department oif fisheries and marine research and the Meteorological Service were trained on aspects of TMDL development and application of the Modeling System. Guidelines, including the manuals provided with the BASINS4 documentation, were developed with specific instructions for the model's application in Cyprus. To publicise the aims and achievements of the project, the organisers held a kick-off seminar attracting 70 participants, three stakeholder consultation workshops and a final conference. Dissemination materials included a project website (www.life-water.eu), a Facebook page (https://www.facebook.com/groups/523204697745618/), a leaflet, an educational brochure, two sign boards, 10 posters, 33 scientific presentations and two popular scientific articles. A ‘Primer on Water Quality Management for Kalo Horio’ was produced, combining the findings and deliverables of the project. This is a useful document for anyone interested in the project and its methodology. Further information on the project can be found in the project's layman report (see "Read more" section).