The use of East African freshwater wetlands for agriculture has increased in recent decades. Agricultural production is highly depending on water quality and quantity and vice versa. Thus, a sound knowledge of the hydrogeological behavior of wetland systems is required providing boundary conditions for sustainable management decisions. Therefore, the presented study aims at a) identifying and explaining hydrogeological processes, b) evaluating the status quo of water quality, and c) assessing the influence of agricultural production on water quality in an inland valley wetland in central Uganda.**Based on geological mapping, drilling surveys, determination of hydraulic conductivity, geochemical analyses, and data acquisition from literature hydrogeological maps, cross-sections, and standard sections were created. Hydrochemical and isotopic analyses of shallow and deep groundwater, stream water, soil water, and precipitation, and groundwater level data, derived from various field campaigns, resulted in a sound understanding of the origins and interactions between different water compartments and water quality aspects.**Two aquifers were identified, the lower part of the alluvial sediments covering the valley itself, and the lower part of the deeply weathered bedrock underlying the sedimentary cover. While regional groundwater flow takes place in the basement aquifer, local groundwater flow in the confined alluvial aquifer is determining wetland hydrogeology. Water quality of the different water compartments is good in terms of drinking water and irrigation purposes. Shallow groundwater is not derived from direct recharge and therefore not vulnerable to water quality deterioration of flooding water due to fertilizer input. Furthermore, no increased amounts of nitrate and potassium were detected in soil water after fertilization (NPK). **Complex hydrogeological processes were successfully visualized in a conceptual model. Moreover, major hazards to water quality related to inputs of fertilizers were outlined. These results can help stakeholders with little hydrogeological knowledge to integrate hydrogeological aspects into agricultural management decisions.**