While the general effects of agricultural land use on riverine biota are well documented, the differential effects of specific crop types on different riverine organism groups, remain largely unexplored. Here we used recently published land use data distinguishing between specific crop types and a Germany-wide dataset of 7748 sites on the ecological status of macroinvertebrates, macrophytes and diatoms and applied generalized linear mixed models to unravel the associations between land use types, crop types, and the ecological status. For all organism groups, associations of specific crop types with biota were stronger than those of urban land use. For macroinvertebrates and macrophytes, strong negative associations were found for pesticide intensive permanent crops, while intensively fertilized crops (maize, intensive cereals) affected diatoms most. These differential associations highlight the importance of distinguishing between crop types and organism groups and the urgency to buffer rivers against agricultural stressors at the catchment scales and to expand sustainably managed agriculture.