In 1204, the city was bought by the Republic of Venice as part of a complicated political deal which involved, among other things, the Crusaders of the Fourth Crusade restoring the deposed Eastern Roman Emperor Isaac II Angelus to his throne. The Venetians improved on the ditch of the city by building enormous fortifications, most of which are still in place, including a giant wall, in places up to 40 m thick, with 7 bastions, and a fortress in the harbour. Heraklion was renamed Candia and became the seat of the Duke of Candia, and the Venetian administrative district of Crete became known as "Regno di Candia" (Kingdom of Candia). To secure their rule, Venetians began in 1212 to settle families from Venice on Crete. The coexistence of two different cultures and the stimulus of Italian Renaissance led to a flourishing of letters and the arts in Candia and Crete in general, that is today known as the Cretan Renaissance. Important buildings built in that era that still survive today are:

The Loggia (noblemen's club) now standing in 25th of August Street, a few yards downhill from the Basilica of St Mark and the Lions square, was constructed in 1626-28 by Francesco Morosini, the same man who built the Lions Fountain. Venetian political and social customs demanded the construction of a public building in Heraklion, as a meeting-place for the nobles, rulers and feudal lords, where economic and commercial decisions were made. It was also a place for them to relax, something like an officers' mess today. The Loggia was the centre of local administrative and social life. From its balconies the heralds proclaimed decrees of state, and the Duke watched the processional litanies and parades. Today the Loggia has been restored to its former glory and houses the Town Hall.

The Basilica of Saint Mark is directly opposite the Lions Fountain, in Eleftheriou Venizelou Square in the centre of Heraklion. Today it houses the Municipal Art Gallery and is open to the public almost all day, every day. From the first years of Venetian rule, in the 13th century (1239), the Venetians, wishing to consolidate their rule over their new colony of Candia and simultaneously express their gratitude to and love of their home, built a basilica dedicated to their patron saint, St Mark. This was where the official ceremonies of the Venetian administration were held, and where the Venetian nobles were buried.

The Venetian harbour of Heraklion is at the end of 25th of August Street, the pedestrian street leading from the town centre to the sea. This is the old harbour of Heraklion, now used by fishing boats and yachts, and its history is as ancient as that of the city itself. In the Venetian harbour of Heraklion stands the fortress of Koules. Here begins the long mole of the new harbour. The mole is a favourite spot for a stroll, especially on warm summer evenings, when the sea breeze offers some relief from the heat. The Venetian harbour also contains the Venetian Arsenals (‘neoria’) or shipyards, where ships were repaired.

One of the first concerns of the Venetian leadership was the supply of water to the thirsty city of Candia, which was lacking in spring water. This was accomplished with the construction of cisterns and wells, public and private ones. Various Venetian fountains are preserved with an elaborate decoration ornamenting the old city of Heraklion. The most noteworthy are: 

Bembo Fountain: Constructed by "capitano" Gianmatteo Bembo between 1552-1554 in today's Kornarou square, next to a later Turkish philanthropic fountain. It is decorated with coats of arms and other elements of the renaissance and of gothic type, while in the middle a big headless statue stands out of the roman period. The spring is ornated with floral and embossed elements.

Sagredo Fountain: Built by Giovanni Sagredo between 1602-1604, part of it has been built in the Northwest corner of today's Loggia (Town Hall) and it is decorated with a carved female statue which was holding a shield in the left hand, and a big hammer in the right one, representing the personification of Crete.

Morosini Fountain: (The so called Lion's fountain). One of the most known fountains of Heraklion, point of reference for its inhabitants, but also for the visitors. Today it is one of the most beautiful monuments of the city. The «General Provisioner» Francesco Morosini built it in 1628, bringing water from the Archanes' springs to the thirsty town of Heraklion. The eight-lobe cistern, which is based on a special stand, is decorated with embossed mythological depictions and maritime figures like tritons, dolphins and various coats of arms. At the very top of the fountain there was a supernatural statue of Poseidon that was standing out but fell probably due to an earthquake. During the Turkish period the fountain went into a vulgar modulation with the addition of a baldachin (ciborium) around it which was later taken away.

Priuli Fountain: The «General Provisioner» Antonio Priuli built it in 1666, in the area of the Venetian Dermata Gate (behind the "Bodosakeio" Primary School) . He decorated it with round and square columns with Corinthian type capitals, while a triangular pediment crowns the whole construction. From both sides of the columns there are niches with their metopes elaborately decorated. In the middle of the fountain there is a Turkish inscription where there is a reference to the name of the Turkish pasha who managed to bring water again in the fountain.