It is most likely that the ability of each to identify the other by sight is something of a literary convention. This is a fairly common thing in antiquity, and especially in the rich Greco-Roman legendary tradition whereby Achaean Greeks and Hittite-speaking Trojans are able to understand one another without fault, just as Aeneas, a Trojan, could to Dido, a Phoenician. In this case, the opposite effect can be seen: total strangers who have no business to know one another are able to fluently converse without issue. The part of ignoring differences and some level of omniscience was, frequently, just part of telling a story, and this especially since the Parable of the Good Samaritan was intended as a moral lesson wherein the identity of the good fellow as a Samaritan was key to the message. Under these circumstances, simply identifying him as a Samaritan as part of the narrative would, essentially, suffice.

I must reinforce that there would be fair difficulty trying to actually identify a Jew from a Samaritan simply by sight in day-to-day non-ritual circumstances. The region was affected by many of the same external and internal influences between both Judea and Samaria, and both groups had pro-Hellenizing and anti-Hellenizing factions warring between one another from within. The same standards for grooming and modesty were held by both groups, based on the common texts and traditions that predated the Babylonian Exile and, while there are some differences expressed between the communities in these, the issues of public appearance are not among them. Even the ritual attire of the two groups was essentially similar at the time.

This is ultimately to say that, no, you would be fairly hard-pressed to be able to consistently distinguish between Jews and Samaritans at a glance given the time period. I mentioned the Parable of the Good Samaritan earlier to drive home a point - that Jesus, or stories about Jesus, tend to have favorable views of the Samaritans and broadly support a stance of reconciliation. The identity of a Samaritan in any Jesus stories is most likely to be an important factor in the message the story is conveying. However, if we take at face value and ask "How does he know that she is a Samaritan?" and assume this is a purely historical incident and not another fable, parable, or otherwise message-bearing story, the answer is simple:

The story is set in Samaria, in the Samaritan cultural capital of Shekhem. To come to the conclusion that she was a Samaritan would be as logical as to assume any random local woman in Jerusalem was a Jew under the same circumstances. There is one difference, however, that may have sealed any sort of attempt at identification: dialect.

You see, both the Samaritans and the Jews spoke Hebrew and Aramaic to varying degrees. In both communities, the final death of Hebrew came around generations after the time of Jesus. Though Aramaic had been known in the public sphere for quite some time and had widespread use as a lingua franca, speaking Hebrew to one another would not be out of the question. In this case, I will point to the word 'water'.

Now, supposing Jesus said something like "Can I have some water?", or just "Gimme a drink of water", the word 'water' has a key difference between Judean and Samarian dialects. The original word, something like *Maym, evolved separately - or, more accurately, the Canaanite Vowel Shift existed on something of a spectrum whereby the Phoenicians took it far, the Jews took it not as far, and the Samaritans took it somewhere between. While it would be typical in Judean Hebrew for earlier *ay to evolve into "e" in line with Phoenician, sometimes it would add an extra vowel instead. The Jewish word for 'water' is "Mayim". The Samaritans, however, spoke Hebrew that took it a bit further - their word for water by contrast would be "Mem". To take Jesus further, the word for 'wine' - "Yayin", in the Samarian dialect is "Yen". So, if we assume this incident to be purely historical, the most reliable way for a Jew and a Samaritan to recognize one another would be simply by the way they talk.