Rural headwater catchments are important to describe the connectivity of pollution sources to water bodies. Strategies to optimize water quality monitoring networks, as parameter definition, sampling, and statistical approach, have been widely discussed. The objectives of this study were to describe the spatial and temporal dynamics (intra- and inter-events) of water quality and to establish its implications for environmental monitoring programs. The monitoring was carried out in a rural headwater catchment (1.2 km2) with shallow soils, high slopes, and intense agricultural activity in Southern Brazil. To better describe the impact of agriculture on water resources, the monitoring strategy was based on definition of the best set of parameters and different sampling frequency to incorporate intra- and inter-event variability and statistical analysis approach. We also analyzed parameters in different sub-basins with physiographic traits. Three hydrological compartments were analyzed: surface flow, groundwater, and base flow. Physico-chemical parameters, the concentration of elements associated with agricultural activity, and biological parameters were evaluated. Total phosphorus and turbidity were the parameters most affected by agricultural activity. They reflected on the inter- and intra-events, the impacts of soil and water degradation by agricultural activity, and the precarious rural sanitation conditions. Spatiotemporal variability of the parameters characterizes the different mechanisms for transferring pollutants from diffuse sources to water bodies. Spatial and temporal patterns in water quality changes were used to discuss environmental monitoring strategies, such as parameter and sampling frequency definition, to improve soil and water conservation programs at the catchment scale.