By using a remotely operated vehicle (ROV), we studied large mucous aggregates produced by the larvacean Bathochordaeus in Monterey Bay, California. These fragile structures or “houses,” cannot be sampled by typical water or net collecting devices, and likely represent a class of cosmopolitan, widely spaced aggregates in subsurface waters. ROV samples allowed us to determine the contribution of the aggregate‐associated communities to populations of microorganisms at depths of 100–500 m. Because the giant houses only average ˜1 per 100 m3, they harbor <1% of the microorganisms in the water, although they are locally enriched. However, once abandoned, houses may play a significant role in transporting materials and organisms to depth. Flux calculations indicate they may seasonally account for 11–100% of some classes of sinking materials at 500 m. These calculations are based on house‐flux contributions predicted from house age (estimated), house abundance (ROV measured), and particle flux (measured by a nearby sediment trap). Based on our ROV observations of spatial and temporal characteristics of the giant aggregates, we calculate the probability that sediment traps collect the correct number of sinking aggregates. Our results suggest that rare particles, such as large aggregates and some sarcodines and pteropods, may be undersampled by commonly used, small sediment traps. Furthermore, the predictably infrequent capture of such comparatively rare particles can lead to erroneous interpretations of temporal or spatial patterns in the flux of material through the upper ocean.