This may be way off, but does the water disperse evenly under the rim, cleaning off the waste after each use. Boy I'll tell you, some people don't realize how much spray gets on the surrounding area of a toilet by this half of the gender, it soaks into tile joints and also creates an odor that can be hard to get rid of. Corrodes radiators, metal partitions, in the last few years of doing some repair work to keep busy, I've seen a lot of bathrooms that are cramped and hard to clean. I've had a similar problem, no change in water though, new toilet on concrete floor in garage, concrete has capillaries and it can absorb, took a good cleaning, no slobs in the house either, this one gets cleaned 1x week and always wiped down with a cleaning spray daily, as does the floor 1x week and for a while this urine like odor would not go away, warmer weather never figured it out, just cleaned, disinfected, solvents on the concrete, finally gone. Seemed like it came out of nowhere, thought the stack vent was clogged or there was another source, can't stand a filthy bathroom that is for sure. One of my customers tenant space had that problem, had to pull the toilet and take the tile up, was a police substation, lot of traffic, sometimes these odors come from years of saturation like at this place, no amount of cleaning would have solved this one. Have never heard of the water turning like that, maybe you can get it tested.
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