Water resources are threatened by many pollution sources. The harmful effects of pollution can be evaluated through biological indicators capable of tracing problems in life forms caused by the contaminants discharged into the streams. In the present study, the effects on stream water quality of landscape configuration, season, and distance from contaminant emissions of diffuse and point sources were accessed through the evaluation of a Portuguese macroinvertebrate index (IPtIN) in 12 observation points distributed within the studied area (Ave River Basin, Portugal). Partial least-squares path models (PLS-PMs) were used to set up cause–effect relationships between this index, various metrics adapted to forest, agriculture, and artificial areas, and the aforementioned emissions, considering 13 distances from the contaminant sources ranging from 100 m to 56 km. The PLS-PM models were applied to summer and winter data to explore seasonality effects. The results of PLS-PM exposed significant scale and seasonal effects. The harmful effects of artificial areas were visible for distances larger than 10 km. The impact of agriculture was also distance related, but in summer this influence was more evident. The forested areas could hold onto contamination mainly in the winter periods. The impact of diffuse contaminant emissions was stronger during summer, when accessed on a short distance. The impact of effluent discharges was small, compared to the influence of landscape metrics, and had a limited statistical significance. Overall, the PLS-PM results evidenced significant cause–effect relationships between land use metrics and stream water quality at 10 km or larger scales, regardless of the season. This result is valid for the studied catchment, but transposition to other similar catchments needs to be carefully verified given the limited, though available, number of observation points.