If you really want to know what you system will be performing I can not recommend doing Spot samples at both end of you system. Unless you have extremly well done tracer test and unless you polution enters you system in a very short time you will not be able really to know when it make sence to take your effluent sample. A more solid approcah will be making Flow Proportional sampling at both influent and effluent over i.e. 24 hours.
On top of that you might take into account using 72h flow proportional samples of in- and effluent. Using this longer sampling period you minimize the influence of the HRT. But this can only be done if you measure parameters that are not degraded easily by microorganisms. When talking about micropollutants 72h samples might be an option e.g. for carbamazepine, for e.g. estradiol the are not. Keeping the sample as cool as possible during sampling is of course even more crucial for this long sampling period.
Q: For sampling in a pollutants removal study what exactly the time should be left between the in fluent and effluent samples? is it the HRT hydraulic retention time
A: It depends on the quality/ quantity of flow - do you have them varying in large %, more than 25% of any parameter, then also you would have the first section the primary one to be a section/ chamber for equalizing the flows.
Inference using a "tracer" can be used at most flows, but the tracer results are difficult to assess as they are mainly floaters, and if surface flow is present then it shows up, if bottom flows are more , then tracer loses its presence,
M&E the Bible of waste-water process, has explained how to get a totally representative sample at in fluent, and effluent. pl do study the same. Also the process, has to have planned upflows to next stage to ensure no by-passing occurs.