Farmland water bodies (FWBs) are marginal habitats in the agricultural landscape. However, regardless of their small size, they are refuges for natural vegetation and species-rich animal assemblages. They are especially important in areas where the intensification of agricultural activities reduces the ecological quality of the landscape. The study aimed to evaluate the effect of the habitat structure of the FWB buffer zone on macrophyte association diversity in the FWBs (n = 49). As many as 175 species of vascular plants, three stoneworts, and 40 (41–49 according to Chao2 estimator) plant associations were recognized, including 19 of high conservation priority. The occurrence of threatened associations (0–5 per FWB) was not correlated with the number of common (unthreatened) ones. The most important predictors of plant diversity (at the species level and the association level) were the connection of the FWB with a watercourse (positive effect), and the distance from the FWB to the nearest built-up areas (positive effect). The results suggest that even though the high percentage cover of perennial vegetation mitigates the effect of diffused pollutions of agricultural origin on FWB biota, its significance may become low when the distance from a built-up area to FWBs is small.