Hey there! I don't know that I qualify as an expert, but as an architect who loves and has studied Japanese architecture a good bit I'll try and provide some background for your question.

Was there a purpose or meaning behind this feature?

So two things here. For purpose we must consider the practicality of such a feature and Japanese domestic life at the time. For meaning we must consider aesthetic and spiritual matters in Japanese domestic life at the time.

On the practicality side of things, consider that in the 1500's there was no indoor plumbing. It seems like an obvious statement but when you need to get your water from either a nearby above ground water source or a well, having it immediately at hand in your home would be super convenient. I have to admit here that it's been years since I've seen Seven Samurai and I don't recall the feature you're mentioning, so I'm kind of presuming off of what I know about traditional home design, but was the creek in the kitchen or the living space? Generally homes were built up off the ground except for some spaces like the kitchen which would be on the ground with a dirt floor. Having a creek pass through here would be simple and useful.

Now, if the creek were in the living space it is less likely that it was a practical feature so much as an aesthetic one, and aesthetics were a big deal back then. To understand traditional Japanese homes you first need to understand the term Wabi Sabi. Wabi Sabi was an aesthetic philosophy that grew up after the introduction of Buddhism in Japan which celebrated the beauty of things like decay, loneliness, etc. I know that sounds grim, it wasn't really viewed that way. It had to do with a recognition of the impermanence of all things, a reverence for self-sacrifice in the name of spiritual awakening, and a respect for nature. In Wabi Sabi, a mug that is irregular/warped and the color of natural clay would be prized above a perfectly round mug glazed in the latest fashions of China (and make no mistake, some of the drive for Wabi Sabi was a nationalistic response to cultural influence from China). A Wabi Sabi philosopher might love and appreciate a particular half-decayed leaf they come upon in the right context, or the patina slowly overcoming a bronze bell, etc. The loneliness aspect too was meant to embody the image of a monk living in a rough cabin in the woods away from society, finding peace and deliverance in nature; rather than a more sort of despondent loneliness. Per Buddhism, it's about appreciation and acceptance of the world around you rather than trying to impose your will over it. So back to an aesthetic indoor creek - this would serve as a constant reminder of Wabi Sabi, reflecting both the constant passage of time (you can never step in the same creek twice) and serving as an indoor reminder of the natural world.

Seems like it would be quite cold in the winters.

This has a related answer to the above when you further examine how Japanese homes were made and lived in. Part of the acceptance of decay and nature wrapped into Wabi Sabi is an acceptance and appreciation for discomfort. The traditional Japanese house is generally made of a wood frame with thin wood walls. In richer examples, the wood would be expertly crafted and the walls would consist of a row of doors with paper screens, called Shoji, that could be opened or even completely removed to appreciate the outdoors and gardens surrounding the house. In poorer areas as can be seen in the movie, the walls would be maybe rough wood plank, woven branches, or perhaps mud. A non-Wabi Sabi reason for this is that wood-framed homes like that stand up better to earthquakes which were frequent. The frame was better able to flex and sway with the quake to minimize the risk of collapse - and if it did collapse was cheaper to rebuild and would do a minimum of damage on the way down. Stone/brick walls, or even mud ones, can't flex and would crumble in an earthquake. But all of this is to say that Japanese homes are already quite cold in the winter. Residents would get through this by dressing more warmly, using small coal braziers to warm the room you're in (or kotatsu, which are a table with a small coal brazier underneath and blankets surrounding it that you can lay in and which capture the heat), and just generally accepting being cold (wabi-sabi). Also keep in mind that Japan is a very large country - southern Japan has a very mild climate compared to the northern regions. I don't know where in Japan Seven Samurai happened off the top of my head, or if Kurosawa even gave it a "place" in the country.

A few sources for further reading I would recommend if you really want to understand this topic more in-depth:

Japanese Homes and Their Surroundings is one of my favorites. It was written by Ed Morse back in the 1800's when it was very popular for Westerners to travel Japan and write books about it. His is notable for an amazing collection of sketches he did while there documenting everything he could about the houses he stayed in. He was also one of the last of his type to do that sort of journey before Japan began to feel the heavy cultural impact of Westernization. The whole thing can be read online here but paper copies aren't too expensive either.

Wabi-Sabi for Artists, Designers, Poets & Philosophers by Leonard Koren does a great job introducing the concepts of Wabi Sabi for a Western mind.

In Praise Of Shadows by Jun'ichirō Tanizaki was a long essay written by a famous Japanese author around the time Kurosawa was making his films where he praised what he saw as Japanese aeshtetic and lamented the impact the Western world had on Japan. Particularly he frames his essay around the contrast for the West's love of light and cleanliness with the Wabi Sabi love of shadow.

The Lessons of Japanese Architecture by Jiro Harada is a very approachable breakdown of a lot of traditional Japanese architecutre

Measure and Construction of the Japanese House by Heino Engel is a more deep-dive into the practicalities of house design and construction.

As an aside, I love Kurosawa's movies so I was glad to see this question. One of my favorite things about his work is his dedication to representing the old lifestyle as accurately as possible as a framework for his stories, even going so far as to rent out preserved "museum towns" that have been kept unchanged for centuries, and filming his entire movies in them. It's so cool to see how the old buildings were used as part of a daily lifestyle rather than to just read about it.