In the film, when Elizabeth arrives at St. Paul's Cathedral, construction is going on. In real life, St. Paul's actually needed repair work. Director Shekhar Kapur decided to improvise, and gave the workers costumes and period tools to cut real stone that was being installed in the cathedral. The workers in the scene are real-life stonemasons and construction workers.
Director Shekhar Kapur felt that color should reveal a character's internal life. Costume designer Alexandra Byrne did not want to use blue on Elizabeth because it was not a period color. Shekhar felt that blue was the color of yearning and aspiring, and he wanted to portray Elizabeth as yearning to be divine and immortal. Likewise, he conveyed Elizabeth's close relationship with Bess by showing them in similar colors and gown styles. As their relationship deteriorates, their colors contrast or clash.
To save money, only one ship replica was built. It was Raleigh's English vessel on one side and a Spanish galleon on the other. When filming wide shots of the deck, smoke was used to cover up any separation in design.
Mary, Queen of Scots, was not originally part of the Babington Conspiracy. Sir Francis Walsingham, who wanted an excuse to have her convicted of a capital crime, got one of the conspirators to act as a double agent and entrap her.
Director Shekhar Kapur filmed Elizabeth's personal time (ex. bathing) in circular sets to reflect the infinite questioning of her mind, aspiring to a different kind of freedom and exploration. He filmed Elizabeth's professional moments (ex. throne room) in rectangular rooms that enclosed her with straight walls and corners.
El Escorial, the Spanish King's palace, is really London's Westminster Cathedral. Since it's a functioning church, the production team had to wait until the last evening confession was done, strip the interior of everything recognizably modern, shoot every scene during the night, then put everything back in place by morning mass.
Though not acknowledged in the credits, the cathedral interiors shown just after the marriage of Sir Walter and Bess are in Wells Cathedral. The camera stops just short of the cathedral's famous "scissor arches."
When Elizabeth is conferring with her advisors about the impending arrival of the Spanish Armada in the large room whose floor is a map (@1:21) on the floor is the Burghley Nef (a partly-gilt salt cellar resembling a late medieval ship sitting atop the back of mermaid who rests on a hexagonal base of rippling waves with six ball-and-claw feet). The Burghley Nef was made in Paris in 1527-28 and rediscovered in Burghley House (home of Lord William Cecil) in 1956.
Elizabeth speaks German to Charles II, Archduke of Austria. There is in fact no historical evidence of Elizabeth having learned German. It is more like that, if they did not converse in English, they would have done so in Spanish, which Elizabeth was known to have learned, and Charles certainly would have, since one branch of the Hapsburg family was Spanish.
All through the story Elizabeth wears wigs. In the pre-battle scene at 1h 28m she is seen to be wearing the hair of a peasant or lower class woman, a World away from the hair of a monarch. The fine suit of armour however, gives the whole game away. Only the much higher classes could afford such.