The magnitude and variability of floods have increased for many nontidal streams on Long Island (LI), NY since the mid-20th century. One of the most densely populated regions of the United States, LI has experienced amplified floods in step with increases in impervious land cover, storm, and sanitary sewers that have accompanied urban development. To better understand the drivers of observed flood trends and effects of urbanization, a nonstationary flood frequency analysis is conducted, using historical annual peak flow records from 17 gaged watersheds on LI using conditional moments based on physical covariates from a two-stage sequential robust linear regression procedure. Regression results indicate that urban development and precipitation are significant co-predictors of peak flows for LI watersheds that have undergone rapid development during the available peak flow record. In watersheds with less intense urbanization or that were fully developed before the peak flow record began, precipitation alone was a significant explanatory variable. Long-term baseflow patterns identified using a nonparametric smoother explained some patterns of decreasing peak flows and heteroskedasticity in the peak flow records. Fitting a log-Pearson III distribution with these conditional moments, floods corresponding to a 20% annual exceedance probability (AEP) are up to 80% higher under a nonstationary framework compared with stationary under current watershed conditions, and differ significantly (95% confidence) from stationary estimates for 6 out of 17 watersheds. Larger floods corresponding to 1% AEPs do not differ significantly between nonstationary and stationary estimates at a 95% confidence level. Nonmonotonic trends observed in two watersheds indicate that recent stormwater management practices, such as rerouting stormwater outfalls away from the channel, substantially reduce flood frequency. Reduced nonstationary flood quantile estimates at these two watersheds are 20 to 40% lower than stationary estimates when accounting for changing watershed conditions over time. Across LI, stormwater management and water-table fluctuations have increased peak flow variability, characteristic of a late phase urban adjustment period on LI. Results of this study demonstrate that a nonstationary framework is a necessary step forward toward a regional flood-frequency analysis for LI. This nonstationary framework will allow flood managers to update flood discharge estimates to current conditions that reflect altered relationships between urban cover and climate for more targeted planning of flood control, transportation infrastructure, and management of floodplain ecosystems.