2 of the best things you can do to ensure good water quality in my opinion are these: have good LR and a good sand bed at least 3' , your deep sand bed will do 3 things first provide a place for processing and exporting some dissolved nutrients. Second, they provide a place to recycle detritus, excess foods, animal feces and other particulate material into useable forms. Finally, they provide a food source for many reef animals.
the sand grain surfaces in our systems provide the major substrate for nutrient processing bacteria. the bacterial population is determined by 3 things. the total sand surface area, the amount of nutrient available and the number and effects of bacterial predators.
a simple way to look at this: One organisms poison is anothers nutrient