Abstract Wetlands protect downstream waters by filtering excess nitrogen (N) generated from agricultural and urban activities. Many small ephemeral wetlands, also known as geographically isolated wetlands (GIWs), are hotspots of N retention but have received fewer legal protections due to their apparent isolation from jurisdictional waters. Here, we hypothesize that the isolation of the GIWs make them more efficient N filters, especially when considering transient hydrologic dynamics. We use a reduced complexity model with 30 years of remotely sensed monthly wetland inundation levels in 3700 GIWs across eight wetlandscapes in the US to show how consideration of transient hydrologic dynamics can increase N retention estimates by up to 130%, with greater retention magnification for the smaller wetlands. This effect is more pronounced in semi-arid systems such as the prairies in North Dakota, where transient assumptions lead to 1.8 times more retention, compared to humid landscapes like the North Carolina Pocosins where transient assumptions only lead to 1.4 times more retention. Our results highlight how GIWs have an outsized role in retaining nutrients, and this service is enhanced due to their hydrologic disconnectivity which must be protected to maintain the integrity of downstream waters.