Investments in renewable energy and smart technologies (such as electric vehicles) totalled $42.4 billion. It is the lowest quarterly total since Q1 2013 when $41.8 billion was invested in clean energy.
The Q3 total was down 31% from the previous quarter and 43% lower than the same period in 2015, BNEF said.
A slowdown in European offshore and Asia were blamed on the lower figures.
"The weakness of Q3 2016 was concentrated in particular areas: asset finance of utility-scale renewable energy projects was down 49% year-on-year at $28.8 billion, with wind down 32% and solar down 67%; and investment in small-scale PV projects of less than 1MW was 35% lower at $9.3 billion," according to BNEF.
"In the geographical split, Chinese investment was down 51% compared with Q3 2015, at $14.4 billion, while Japan was down 56% at $3.5 billion," it added.
BNEF analyst Abraham Louw said: "There is one special factor here, in the timing of offshore wind financings in Europe. These totalled $20.1 billion in the first six months of 2016, a runaway record. But there was then a summer lull, with just $2.4 billion in July to September."