This study investigates the impact of pesticide use on bee diversity and the potential role of non-crop habitats in mitigating these effects in the Kole paddy wetlands, a Ramsar site in Kerala, South-West India. Bee populations were sampled over two years, in six pesticide treated and six non-treated control fields, along with adjacent bunds as non-crop habitats. A total of 173 bees representing 10 species across two families—Halictidae and Apidae—were collected. Species richness and Shannon diversity, were consistently lower in pesticide-treated fields compared to control fields. Non-Metric Multidimensional Scaling (NMDS) showed a distinct clustering of treated sites, indicating homogenized bee communities dominated by species such as Tetragonula sp. and Apis florea. In contrast, species like Halictus sp. were less common in treated fields. The bunds with dense vegetation, adjacent to treated fields showed a positive correlation with bee diversity, suggesting these areas act as refugia against pesticide exposure. Pearson correlation analysis revealed a significant positive relationship (r = 0.8389, p = 0.0369) between the diversity of treated fields and their adjacent non-crop habitats. Our findings signify the need for integrated pest management strategies that reduce pesticide use and promote the conservation of non-crop habitats, such as bunds to support pollinator populations, thereby ensuring the overall health and functioning of Kole paddy wetlands.