Many populated, tropical coastlines fronted by fringing coral reefs are exposed to wave-driven marine flooding that is exacerbated by sea-level rise. Most fringing coral reef are not alongshore uniform, but bisected by shore-normal channels; however, little is known about the influence of such channels on alongshore variations on runup and flooding of the adjacent coastline. We con-ducted a parametric study using the numeric model XBeach that demonstrates that a shore-normal channel results in substantial alongshore variations in waves, wave-driven water levels, and the resulting runup. Depending on the geometry and forcing, runup is greater either on the coastline adjacent to the channel terminus or at locations near the alongshore extent of the channel. The impact of channels on runup increases for higher incident waves, lower incident wave steepness, wider channels, a narrower reef, and shorter channel spacing. Alongshore varia-tion of infragravity waves is predominantly responsible for large-scale variations in runup out-side the channel, whereas setup, sea-swell waves, and very-low frequency waves mainly increase runup inside the channel. These results provide insight into which coastal locations adjacent to shore-normal channels are most vulnerable to high runup events, using only widely available data such as reef geometry and offshore wave conditions.