Loss of reef roughness increases residence time on an idealized coral reef

<jats:title>Abstract</jats:title><jats:p>Through idealized, numerical models this paper investigates flows on a reef geometry which has received significant attention in the literature; a shallow, fringing reef with deeper, shore-ward pools or lagoons. Given identical model geometries and varying only reef flat drag coefficients between model runs (<jats:inline-formula><jats:alternatives><jats:tex-math>$$C_D = [0.001,0.005,0.01,0.05,0.1]$$</jats:tex-math><mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:msub> <mml:mi>C</mml:mi> <mml:mi>D</mml:mi> </mml:msub> <mml:mo>=</mml:mo> <mml:mrow> <mml:mo>[</mml:mo> <mml:mn>0.001</mml:mn> <mml:mo>,</mml:mo> <mml:mn>0.005</mml:mn> <mml:mo>,</mml:mo> <mml:mn>0.01</mml:mn> <mml:mo>,</mml:mo> <mml:mn>0.05</mml:mn> <mml:mo>,</mml:mo> <mml:mn>0.1</mml:mn> <mml:mo>]</mml:mo> </mml:mrow> </mml:mrow> </mml:math></jats:alternatives></jats:inline-formula>), two distinct circulation patterns emerge. One is related to low reef water levels and high roughness, and efficiently flushes the entire reef system resulting in low residence times (an ‘open reef’). The other is related to high reef water levels and low roughness, and in spite of the development of an offshore undertow, this dynamic is inefficient at flushing the reef-pool system and facilitating exchange flow with offshore waters (a ‘closed reef’). This paper shows that even given indistinguishable geometry and offshore conditions, this information is insufficient to predict reef dynamics, and suggests that reef roughness (and thus reef health) plays a comparable role in determining circulation patterns and residence times. Furthermore, a transition from open to closed or vice versa caused by e.g., a loss of reef roughness or increase in mean sea level could have implications for transport and mixing of nutrients and water masses, as well as larval dispersal.</jats:p>