Nine cycling routes, which in sections satisfy the description of a cycling path in some sections, run through the city boundaries; they are marked with the numbers 12, 122, 1018, 1050, 1092, 1100, 1108, 1109 and 1120 and shown on the “Cycling map“ which is located on the corner of Gerstnera Street and Zátkovo Embankment in front of the entrance to Háječek.
- Route no. 12 running in the north to south along the Vltava River (it is a part of the bike path which runs through the Czech Republic from Germany to Austria);
- Route no. 122 in the northern part of the city along the right bank of the Vltava River in the direction of Borek and then all the way to Třeboň;
- Route no. 1018 running along the right bank of the Malše River in the direction of Vidov;
- Route no. 1050 in the direction of Dobrá Voda;
- Route no. 1096 in the direction of Rudolfov;
- Route no. 1092 in the direction of Litvínovice, Lipí;
- Route no. 1100 in the direction of Dubné;
- Route no. 1108 in the direction of Vrbenské rybníky;
- Route no. 1120 in the direction of St. Hodějovice, Ledenice.
New city cycle routes built in 2003 (already completed) and 2004/2005 (under construction) are marked with capital Latin letters (A – J) for clarity. Cycle route A - is a route by-passing the city centre and closing a part of the bypass formed by bike path no. 12. The start of the cycle route is connected with bike path no. 1018 on the Malše River Embankment near the historical building of the South-Bohemian Theatre. The route runs along Jirsíkova Street and across Dukelská and Karla IV Streets, and then follows Mlýnská Canal, where it runs through a park along an existing park path which is at least 3 metres wide. Cycle route B - connects the city centre with the Strakonická shopping zone. Cycle route C - runs radially from the city centre along Jírovcova Street – in the future it is expected to be connected with route D between Pražské Suburb and the Husova kolonie neighbourhood. Cycle route D - runs tangentially along the northern edge of the inner city connecting the B and C cycle routes. Cycle route E - connects the city centre and the central part of Suché Vrbné neighbourhood and continues to Rudolfovská Road (the problem regarding crossing Novohradská Street, the foot bridge over the railway and the Ledenická road is yet to be solved). Cycle route F - connects the city centre with Stromovka Park and continues to Máj Housing Estate along bike path no. 1100. Cycle route G - connects the city centre with the Šumava and Máj housing estates via Dlouhý Bridge (the problem regarding crossing Dlouhý Bridge and J. Opletala Street has not been solved yet). Cycle route H - provides connection with the Vltava Housing Estate via cycle route G (the crossing of Husova Street is a problem that is yet to be solved). Cycle route I - this cycle route connects the H and B cycle routes. Cycle route J - runs on the side of existing streets and roads and connects cycle route I with cycling path no. 122 and also with the second part of cycle route B – in the area of Suchomelská Street. Another cycle route is planned along the left bank of the Vltava River from the sports hall to Stecher Mill. Within the frame of the city system, this bike path is going to be connected with Poliklinika Jih (an outpatient medical centre) by means of a crossing over the Vltava River, along E. Pittera Street. In addition to that, the town, in cooperation with several neighbouring villages (Roudné, Vidov etc.), intends to try to build a bike path along the left bank of the Malše River, similar to the one connecting the city with Hluboká nad Vltavou.