halacha - Counting Sefiras Haomer in the Bathroom

If one is (stuck) in a bathroom with a short amount of time left until sunset, and realizes that he has not yet counted Sefirah for that day, and will not be out of the bathroom before sunset, may he count in the bathroom?

Answer

Terrific question. I found a discussion of the issue by Rabbi S.B. Genut (in the case of someone locked in a bathroom) here, which I'll summarise for those for whom Hebrew is a barrier.

Firstly, we'll assume that a modern bathroom is considered a place of uncleanliness (which is a discussion in itself, since our bathrooms are pretty clean compared to those in olden times).The Mishna B'rura (Biur Halacha OC 588 s.v. שמע ט' תקיעות) quotes the Mateh Efraim (a classic work on the laws of the Days of Awe) that if someone became incontinent while blowing the shofar, he should stop. The MB asks why - after all, why should this automatically be like shema or tefillin where we explicitly are commanded to read/wear it in a clean place? It's not forbidden to do other mitzvot in an unclean place - we don't take off tzitzit when entering a bathroom.

He suggests that it might be because of מצוות צריכות כוונה, mitzvot requiring thought (as @DonielF floated in the comments). However, many hold that Rabbinical mitzvot don't require kavana, and that counting the Omer in our times is rabbinical. (Which is why if you accidentally say what day it is in answer to someone's question, you don't count with a bracha.) So he suggests that one may count without kavana (and obviously without a blessing).

However, he notes that the שו"ת מעט מים (which I think was by R' Avraham of Salonica, who was among those expelled from Spain in 1492) discusses the issue and forbids it because one cannot possibly do a mitzva without thinking about it, and that is no different from thoughts of Torah.

Another reason the MB quotes is that this might just be disrespectful of the mitzva. (Similarly, it is brought that it is forbidden to use urine to wash/sterilise a shofar [which apparently was something people did back then!] because it is disrespectful.) However, R' Genut says that if this will cause you to miss out on counting for the rest of the sefira, there is room to be lenient, just like with an onen (as @Danny Schoemann mentioned, though he sources it to the Noda B'Yehuda Mahdura Kama OC 27).

He also quotes R' Chaim Palachi (in Lev Chaim 2:123, Moed L'Kol Chai 5:6), asked about one who is imprisoned in an unclean place. He says that one may count without a bracha, just like one may give charity or slaughter an animal in an unclean place.

Finally, he notes that he asked someone to ask R' Chaim Kaniyevski shlita, who said that one may not. But there are claims that on another occasion he ruled that one may.