Invertebrate colonization in a shallow estuarine embayment was studied with the use of artificial substrates (bottle brushes) to create and mimic complex habitats. Substrates were manipulated to obtain varying levels of habitat density and surface area by shortening and/or removing bristles from the brushes. Complexity was quantified as the total surface area of bristles and bristle surface area within the geometric volume of the substrate (i.e., bristle density). Short-bristled brushes provided greater habitat density while long-bristled brushes provided larger surface area within the same removal treatment. Abundance of invertebrates that recruited from the water column (mostly from the meiobenthos) averaged 2500–7000 individuals per collector after 10 days, and abundances significantly increased with increasing habitat density (i.e., decreasing bristle removal). The abundance of nematodes and copepod species richness were more closely related to bristle density than surface area. Copepod abundance was more closely related to surface area than bristle density. Flow visualizations in a paddlewheel flume revealed that water was diverted around brushes with high bristle density (0% and 20% bristle removal), regardless of bristle length, when incident flow was 6 cm s−1. Relatively more water passed through the brushes in low bristle density treatments (80% removal) and when freestream velocity was increased to 12 cm s−1. Measurements of flow speed on the upstream and downstream sides of brushes confirmed that fractional transmission of velocity (transmissivity) increased with freestream velocity, but showed inconsistent patterns among length and removal treatments. Flow was substantially decreased by interaction with the brushes, which probably enhanced the retention of invertebrates. The dissimilar responses of nematodes and copepods suggest that not all small taxa respond to the same components of architectural complexity and that there are both physical and biological components to recruitment of these artificial substrates.