GEMARA

(Beraisa - Tana d'Vei R. Yishmael): It says (regarding Simanim of Kosher fish) twice "ba'Mayim" (and afterwards, Pratim). Therefore, we do not expound according to Klal u'Frat (general and specific terms), rather, according to Ribuy and Mi'ut (inclusions and exclusions):

Chulin 66b (Beraisa) Question: What is the source to permit fish (even without Simanim, i.e. fins and scales) in Kelim?

Answer #1: "This you will eat, among all that is in water... (in seas and rivers)" - in seas and rivers, we may eat only fish with Simanim, but in Kelim, we may eat fish even without Simanim.

"In water" is a Klal. "In seas and rivers" is a Prat. "In water" is another Klal;

(Ravina): Chachamim of Eretz Yisrael teach that we may insert a Prat between two adjacent Klalim to make a Klal u'Frat u'Chlal.

We learn cases like the Prat, i.e. flowing water. This includes (to forbid fish without Simanim in flowing) Charitzim and Ne'itzim (long pits or quarries. All) fish in (still) pits are permitted.

Question: Perhaps the Prat is bodies of water (in the ground, not in Kelim), and all such cases are forbidden!

Answer: If so, the repetition "you may eat" would not teach anything.

Answer #2 (Tana d'Vei R. Yishmael): We do not expound "in water... in water" according to Klal u'Frat, rather, like Ribuy and Mi'ut;

"In water" is a Ribuy. "In seas and rivers" is a Mi'ut. "In water" is another Ribuy. We (initially) include everything, i.e. we forbid (fish without Simanim) in Charitzim and Ne'itzim. We exclude pits (of still water, to permit).

Question: Perhaps pits are included (to forbid fish without Simanim), and Kelim are excluded (to permit fish without Simanim)!

Answer: If so, the repetition "you may eat" would not teach anything.

Question: We should say oppositely, that pits are included to forbid, and Charitzim and Ne'itzim are excluded to permit!

Answer (Matisyahu ben Yehudah's Beraisa): We include pits to permit, for they are still water, like Kelim. We exclude Charitzim and Ne'itzim and forbid, for they are not still, unlike Kelim.

RISHONIM

Rambam (Hilchos Ma'achalos Asuros 2:18): If a water Sheretz was created in a pit, since the water does not flow, and it is still, this is like water in Kelim, so it is permitted. One may bend down and drink water from a pit, even though he swallows some small Sheratzim.

Magid Mishneh: The Rambam forbids Charitzim and Ne'itzim that are not still, even if they do not flow. He permits only pits, which are still, like Kelim. He explains like Tosfos, and rules like R. Yishmael. The Sifra supports him. The Rashba agrees.

Rambam (20): One need not refrain from drinking wine, vinegar or beer due to worms inside.

Rosh (Chulin 3:68): Tosfos says that according to Tana d'Vei R. Yishmael, who expounds Ribuy and Mi'ut, we forbid even Charitzim and Ne'itzim that do not flow. According to Tana d'Vei Rav (the first Tana; also in Rashi's text, this is Tana d'Vei Rav), who expounds Klal u'Frat, we permit Charitzim and Ne'itzim, since they do not flow. Also according to this Perush, it seems that the Halachah follows Tana d'Vei Rav, for it was fluent in people's mouths, against Tana d'Vei R. Yishmael.

Ma'adanei Yom Tov (80, based on Rashi 66a DH Tana): Answer #1 was from Tana d'Vei Rav, i.e. Sifra (Beraisos that expound verses in Vayikra).

POSKIM

Shulchan Aruch (YD 84:1): Sheratzim that grow in water in Kelim and pits that do not flow are permitted, even if they do not have fins and scales. Therefore, one may bend down and drink from them, without concern lest Sheratzim come to his mouth.

Shach (1): The same applies to other liquids. The Rambam, Hagahos Maimoniyos and other Poskim say so.

Taz (2): Isur v'Heter ha'Aruch says that if they disgusthim,or there is danger, it is forbidden due to Bal Teshaktzu. Also the Rambam (Hilchos Rotze'ach 11:6) and Maharshal say so.

Shach (3): The Shulchan Aruch connotes that there is no problem of Bal Teshaktzu. Sefer ha'Chinuch explicitly says so. The Rema (13:1) forbids eating live fish, but here he intends only to drink, and he does not overtly swallow fish.

Shulchan Aruch (2): Some forbid fish that grow in Charitzim and Ne'itzim (pits that are long and thin, or wide, like fish quarries) that are Moshech but do not flow, and some permit.

Shach (2): It does not depend on the shape of the pit. It depends only on whether it is Moshech, i.e. it has Motza u'Va.

Mishbetzos Zahav (Reish ha'Siman): Motza u'Va means that it has a source, e.g. when there is much rain,water drips to it, and from it to another place.

Beis Yosef (DH Sheratzim): Rashi connotes that there is no argument between the first Tana and Tana d'Vei R. Yishmael. All agree that we forbid Charitzim and Ne'itzim only if they flow. We permit if they do not flow, for then they are unlike seas and rivers. Tosfos challenged this. If so, why did the Gemara say that it depends on whether the water is still? It should include and forbid Charitzim and Ne'itzim, which flow, like seas and rivers! Rather, we discuss Charitzim and Ne'itzim that do not flow. This is why the Gemara asked why they are different than regular pits! It answered that even though they do not flow, they are like seas and rivers, for they are not still. The one who expounds Ribuy u'Mi'ut includes to forbid Charitzim and Ne'itzim that do not flow, and permits regular pits. The one who expounds Klal u'Frat includes to permit even Charitzim and Ne'itzim that are not still like Kelim, since they do not flow. The Rosh says that even according to Tosfos, the Halachah follows the first Tana. However, the Magid Mishneh says that the Rambam rules like R. Yishmael.

Taz (Reish ha'Siman): The Tur says that the Rambam permits only in (regular) pits; the Rosh says otherwise. It seems that also the Rambam holds like Tana d'Vei Rav, but the Rambam holds that all forbid Charitzim that do not flow, but are Moshech and Zochel (flow very slowly). Tana d'Vei Rav and Tana d'Vei R. Yishmael argue about Charitzim that do not flow and are not Moshech. Tana d'Vei Rav considers these like pits, and Tana d'Vei Rav forbids, for they are big and unlike Kelim. Elsewhere, we say that a Keli that holds more than 40 Sa'im is not considered a Keli! The Tur learned from the repetition in the Rambam 'the water does not flow, and it is still, like Kelim.' This teaches that even if the water does not flow, if it is Zochel, it is forbidden like flowing water. It is permitted only if it is still. This applies even to Charitzim. The Rambam said so about pits, for they are surely still. The Tur says that the Rosh disagrees, for he does not forbid Charitzim ha'Moshchim as if they flow. He forbade only what truly flows. Also the Ran connotes that the primary Chidush is that Zochelim are like flowing.

Shach (8): The Maharshal is stringent, and it seems that also Isur v'Heter ha'Aruch is stringent.