The greatly increased use of aquatics species to study disease over the past 20 years necessitates understanding their husbandry and housing requirements to optimize research and welfare and ensure compliance with regulations. To achieve these goals, aquatics systems have expanded from pet shop and home aquaria to research grade systems incorporating designs and features to increase their robustness, practicality, and flexibility. Moreover, these last decades have seen the increasing use of aquatic animals for infectious disease research using containment level 2/biosafety level 2 (CL2/BSL2) pathogens. Here, we discuss the facility design requirements and modifications which must be considered for the planning, construction and use of an aquatics facility for zebrafish infected with CL2 pathogens. These include decontamination of water and equipment, racking and filtration design, personal protective equipment, and husbandry procedures. This guidance is based on our experience in the design and ongoing management of such facilities.