Nuhtty... the flow likely needs increased for this refugium in two principal areas. The "calm" zone at the bottom is a concern in almost any/every tank (excessively accumulating nutrients/solids over time) except for bare-bottomed vessels that are specifically acting as a settling chamber and get serviced regularly (siphon detritus weekly or more often).
Make a concerted effort to keep solids in suspension for processing by filterfeeders or exporting (via skimmers, mechanical filters,etc.).
My other area of concern is the live rock/rubble "prefilter" of incoming water. This honestly serves no practical purpose but instead tends to handicap the system (trapping detritus over time or simply nitrifying matter when we'd rather it got consumed directly, or exported as per above.
Very nice diagram too! Thanks for sharing
Anthony