Shelter availability is one of the key features governing crayfish habitat quality. It can directly influence crayfish's individual survival of by lowering the risk of predation, but the ecosystem-wide impacts of sheltering on water quality are largely unknown. To test the effects of shelter availability for Procambarus clarkii in clear-water macrophyte-dominated lakes, we performed a 24-day mesocosm experiment in 20 tanks (4 with one crayfish with and without shelters, 4 with two crayfish with and without shelters and 4 controls). The bottom of each tank was almost completely covered by the eelgrass Vallisneria denseserrulata. Compared with the treatments with shelters, more broken leaves occurred in the treatments without shelters at both crayfish densities at equivalent crayfish numbers, and total phosphorus was higher in the treatments without shelters. Total suspended solids and total nitrogen concentrations were higher in the treatments with two crayfish without shelters than in those with shelters, whilst these variables did not differ between treatments in the mesocosms with one crayfish only. Our results suggest that shelter availability reduces the activity of crayfish (e.g. movement and burrowing) and agonistic behaviour, thereby decreasing the negative effect of the invasive P. clarkii on water quality in V. denseserrulata-dominated clear-water lakes.