The Lonja rises in the Kalnik mountain in northern Croatia, southeast of Novi Marof, at . It flows westward until turning south near Breznički Hum, passing east of Sveti Ivan Zelina, and turning southeast near Sveta Helena. East of Lupoglav, it turns south again, passing through Ivanić-Grad and nearing the river Sava.
It then flows in parallel to the Sava for the rest of its course, and the nature park Lonjsko polje, a protected area, covers the remainder of the Lonja river basin. Near the end of its course, the river splits into Stara Lonja ("Old Lonja") that enters Sava at the eponymous village of Lonja; and Trebeš or Trebež that discharges into Sava some 5.5 km downstream in the eponymous village of Trebež at .[maps 1]
The main tributaries of the Lonja are:
- Česma (Čazma) (124 km long), which joins Lonja northeast of Sisak
- Ilova (85 km long), at Trebež, south of Kutina
- Pakra, at Trebež, south of Kutina
- Zelina, south of Ivanić-Grad
- Ostroški, Ljiljana, ed. (December 2015). Statistički ljetopis Republike Hrvatske 2015 [Statistical Yearbook of the Republic of Croatia 2015] (PDF). Statistical Yearbook of the Republic of Croatia (in Croatian and English). 47. Zagreb: Croatian Bureau of Statistics. p. 49. ISSN 1333-3305. Retrieved 27 December 2015.
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