Rivers receive and process large quantities of terrestrially derived organic matter. Global studies using standardized cotton strip assays show that organic matter processing varies widely across biomes, is fastest at low latitudes, and is consistently higher in rivers than in adjacent riparian zones, reflecting differences in temperature sensitivity and moisture limitation. Despite the importance of tropical rivers to global runoff and carbon emissions, organic matter processing in tropical stream and riparian systems remains understudied, particularly across seasons and land-cover types. We examined seasonal shifts in organic matter processing across forested, pasture (intermittent and perennial), and urban streams and adjacent riparian zones in southern Mexico using a standardized cotton strip assay deployed during the wet and dry seasons of 2023. We predicted higher processing rates in streams than in riparian zones, strong seasonal effects, and elevated instream decomposition in urban systems, particularly during the dry season. We also expected higher processing rates in perennial than in intermittent pasture sites. Instream processing rates were high relative to other tropical sites, especially in urban streams during the dry season under hotter, drier conditions. As expected, processing rates were consistently higher in streams than in riparian zones, which exhibited uniformly low rates and weak responses to season and land cover. Seasonality was the dominant driver of organic matter processing, with substantially higher decomposition during the wet season across land cover types. Urban land cover exerted a strong but season-dependent effect, with the highest instream decomposition rates overall. Contrary to expectations, intermittent pasture streams did not show reduced instream processing during the dry season relative to perennial streams, despite flow intermittency. Together, these results indicate that seasonal hydrology is the primary regulator of organic matter processing in tropical stream and riparian systems. Additionally, urbanization amplifies instream decomposition relative to forested and pasture systems, with differences especially pronounced during the dry season. Because stream research in the tropics is often conducted during the dry season, our findings suggest that seasonal sampling bias may lead to systematic underestimation of organic matter processing in tropical watersheds and their contribution to global organic matter processing.