I would also suggest running the water throughout the house to clear the lines. If the issue is isolated to you, there could be an issue with the lines running to the house. Before it rains, see if you have any wet spots where your lines should be running. You can also consult a plumber that has the technology to run a camera through your outside lines to look for a crack that could be allowing sediment into the lines. Good luck!

Thanks for the thoughts and ideas. The water appears this weird color in two separate toilets and in two separate tubs/showers. It's hard to tell whether the water is off-color running out of the kitchen faucet as well.

I recently went to visit my brother and we stayed in the wing of the house where his now college kids used to be. We went to give our kids a bath in the tub. Since their cousins are all older, they only take showers. I switched the water to the tub faucet and it came out brown and green. Pretty disgusting. But we let the water run about 5 minutes and the water came out clear. My brother guestimated that that it had likely been 6-7 years since anyone took a bath in the tub and that was just crud/rust/build-up in the fixture. I would suggest running the toilet and propping the toilet flapper up for about 5 minutes and letting it run water through the system. Was the house unoccupied for several months between when the sellers moved out and when you moved in? Or is the toilet one that they would not have used much? Do you have this problem in any other faucet in the house (kitchen sink, master bath, etc)? If not then this is likely just a problem with the one fixture that wasn't used much.

Whoops, just noticed you said it's in the toilet, so likely not the hot water heater.

Is it hot water? Cold water? Or both? If it's just hot, it could be the hot water heater.

Thanks PP. I'm not sure if we have copper pipes. Where do we start to diagnose the problem? The County flushed the lines last night which did nothing to improve the problem and only made the water more greenish/brown for a bit. Now, it's back to the same greenish tint. Other ideas? Is there a good plumber to detect this kind of issue.

do you have copper pipes

http://safewater.supportportal.com/link/portal/23002/23015/Article/14391/What-can-cause-tap-water-to-appear-blue-green

We just moved into a 1957 house in North Arlington in a really forested part of the area and noticed that the water in the toilet is not clear - it's sort of a beigy/green color. We also noticed this when running the water in the bathtubs. We hadn't noticed this when considering buying the house as the toilet and tub were pink (they're now white thanks to some tile glazing). We asked the neighbor whether they had any issue and they said they didn't. The inspector didn't note any issue and the sellers certainly never flaggesd this. We're now starting to think it's a problem specific to the house. Because we have young kids, and have read enough online about pipe corrosion, lead, etc, we're getting a little worried. We called the county and they've "never heard of green water before!" Any ideas or experience with this? Thanks in advance.