Suburbanization negatively impacts aquatic systems by altering hydrology and nutrient loading. These changes interact with climate and aquatic ecosystem processes to alter nutrient flux dynamics. We used a long term data set (1993–2009) to investigate the influence of suburbanization, climate, and in-stream processes on nitrogen and phosphorus export in rivers draining the Ipswich and Parker River watersheds in northeastern MA, USA. During this timeframe population density increased in these watersheds by 14 % while precipitation varied by 46 %. We compared nutrient export patterns from the two larger watersheds with those from two nested headwater catchments collected over a nine year period (2001–2009). The headwater catchments were of contrasting, but stable, land uses that dominate the larger watersheds (suburban and forested). Despite ongoing land use change and an increase in population density in the mainstem watersheds, we did not detect an increase in dissolved inorganic nitrogen (DIN) or PO₄concentration or export over the 16-year time period. Inter-annual climate and associated runoff variability was the major control. Annual DIN and PO₄export increased with greater annual precipitation in the Ipswich and the Parker River watersheds, as well as the forested headwater catchment. In contrast, annual DIN export fluxes from the suburban headwater catchment were less affected by precipitation variability, with inter-annual export fluxes negatively correlated with mean annual temperature. The larger watershed exports diverged from headwater exports, particularly during summer, low-flow periods, suggesting retention of DIN and PO₄. Our study shows suburban headwater exports respond to inter-annual variation in runoff and climate differently than forested headwater exports, but the impacts from headwater streams could be buffered by the river network. The net effect is that inter-annual variation and network buffering can mitigate higher nutrient exports from larger suburbanizing watersheds over decadal time periods.