Margao, like the rest of Goa, has a short tourist season running from November to March. The monsoon arrives in June and stays until September, bringing heavy rain that turns the market lanes into streams and makes the countryside intensely green. October and April are shoulder months — fewer visitors, lower prices, and weather that is either cooling down or heating up.
November through February is the most comfortable time: warm days, cool evenings, and clear skies. The feast of the Holy Spirit at the Church of the Holy Spirit falls in June (Whit Monday), meaning the church is at its most festive just as the monsoon is arriving. If you are in Goa for the beach resorts, Margao makes a good half-day excursion at any time of year — the market and the old quarter work regardless of season.